The mutation process ultimately defines the genetic features of all populations and, hence, has a bearing on a wide range of issues involving evolutionary genetics, inheritance, and genetic disorders, including the predisposition to cancer. Nevertheless, formidable technical barriers have constrained our understanding of the rate at which mutations arise and the molecular spectrum of their effects. Here, we report on the use of complete-genome sequencing in the characterization of spontaneously arising mutations in the yeast Saccharomyces cerevisiae . Our results confirm some findings previously obtained by indirect methods but also yield numerous unexpected findings, in particular a very high rate of point mutation and skewed distribution of base-substitution types in the mitochondrion, a very high rate of segmental duplication and deletion in the nuclear genome, and substantial deviations in the mutational profile among various model organisms.

Speciation involves the origin of trait differences that limit or prevent gene exchange and ultimately results in daughter populations that form monophyletic or exclusive genetic groups. However, for recently diverged populations or species between which reproductive isolation is often incomplete, gene genealogies will be discordant, and most regions of the genome will display nonexclusive genealogical patterns. In these situations, genome regions for which one or both species are exclusive groups may mark the footprint of recent selective sweeps. Alternatively, such regions may include or be closely linked to “speciation genes,” genes involved in reproductive isolation. Therefore, comparisons of gene genealogies allow inferences about the genetic architectures of both reproductive isolation and adaptation. Contrasting genealogical relationships in sexually isolated pheromone strains of the European corn borer moth ( Ostrinia nubilalis ) demonstrate the relevance of this approach. Genealogies for five gene regions are discordant, and only one molecular marker, the sex-linked gene Tpi , has evidence for pheromone strain exclusivity. Tpi maps to a position on the sex chromosome that is indistinguishable from a major factor ( Pdd ) affecting differences in postdiapause development time. The major factor ( Resp ) determining male behavioral response to pheromone is also sex-linked, but maps 20-30 cM away. Exclusivity at Tpi may be a consequence of these linkage relationships because evidence from phenotypic variation in natural populations implicates both Pdd and Resp as candidates for genes involved in recent sweeps and/or reproductive isolation between strains.

Thomas Hunt Morgan and colleagues identified variation in gene copy number in Drosophila in the 1920s and 1930s and linked such variation to phenotypic differences [Bridges CB (1936) Science 83:210]. Yet the extent of variation in the number of chromosomes, chromosomal regions, or gene copies, and the importance of this variation within species, remain poorly understood. Here, we focus on copy-number variation in Drosophila melanogaster . We characterize copy-number polymorphism (CNP) across genomic regions, and we contrast patterns to infer the evolutionary processes acting on this variation. Copy-number variation in D. melanogaster is nonrandomly distributed, presumably because of a mutational bias produced by tandem repeats or other mechanisms. Comparisons of coding and noncoding CNPs, however, reveal a strong effect of purifying selection in the removal of structural variation from functionally constrained regions. Most patterns of CNP in D. melanogaster suggest that negative selection and mutational biases are the primary agents responsible for shaping structural variation.

Of 12 potential reproductive isolating barriers between closely related Z‐ and E‐pheromone strains of the European corn borer moth (Ostrinia nubilalis), seven significantly reduced gene flow but none were complete, suggesting that speciation in this lineage is a gradual process in which multiple barriers of intermediate strength accumulate. Estimation of the cumulative effect of all barriers resulted in nearly complete isolation (>99%), but geographic variation in seasonal isolation allowed as much as ∼10% gene flow. With the strongest barriers arising from mate‐selection behavior or ecologically relevant traits, sexual and natural selection are the most likely evolutionary processes driving population divergence. A recent multilocus genealogical study corroborates the roles of selection and gene flow ( Dopman et al. 2005 ), because introgression is supported at all loci besides Tpi, a sex‐linked gene. Tpi reveals strains as exclusive groups, possesses signatures of selection, and is tightly linked to a QTL that contributes to seasonal isolation. With more than 98% of total cumulative isolation consisting of prezygotic barriers, Z and E strains of ECB join a growing list of taxa in which species boundaries are primarily maintained by the prevention of hybridization, possibly because premating barriers evolve during early stages of population divergence.

The E and Z pheromone strains of the European corn borer (ECB) provide an exceptional model system for examining the genetic basis of sexual isolation. Differences at two major genes account for variation in female pheromone production and male behavioral response, components of the pheromone communication system known to be important for mate recognition and mate choice. Strains of ECB are morphologically indistinguishable, and surveys of allozyme and DNA sequence variation have revealed significant allele frequency differences at only a single sex-linked locus, Tpi. Here we present a detailed genetic linkage map of ECB using AFLP and microsatellite markers and map the factors responsible for pheromone production (Pher) and male response (Resp). Our map covers 1697 cM and identifies all 31 linkage groups in ECB. Both Resp and Tpi map to the Z (sex) chromosome, but the distance between these markers (>20 cM) argues against the hypothesis that patterns of variation at Tpi are explained by tight linkage to this “speciation gene.” However, we show, through analysis of marker density, that Tpi is located in a region of low recombination and suggest that a second Z-linked reproductive barrier could be responsible for the origin and/or persistence of differentiation at Tpi.

Copy-number variants (CNVs) reshape gene structure, modulate gene expression, and contribute to significant phenotypic variation. Previous studies have revealed CNV patterns in natural populations of Drosophila melanogaster and suggested that selection and mutational bias shape genomic patterns of CNV. Although previous CNV studies focused on heterogeneous strains, here, we established a number of second-chromosome substitution lines to uncover CNV characteristics when homozygous. The percentage of genes harboring CNVs is higher than found in previous studies. More CNVs are detected in homozygous than heterozygous substitution strains, suggesting the comparative genomic hybridization arrays underestimate CNV owing to heterozygous masking. We incorporated previous gene expression data collected from some of the same substitution lines to investigate relationships between CNV gene dosage and expression. Most genes present in CNVs show no evidence of increased or diminished transcription, and the fraction of such dosage-insensitive CNVs is greater in heterozygotes. More than 70% of the dosage-sensitive CNVs are recessive with undetectable effects on transcription in heterozygotes. A deficiency of singletons in recessive dosage-sensitive CNVs supports the hypothesis that most CNVs are subject to negative selection. On the other hand, relaxed purifying selection might account for the higher number of protein–protein interactions in dosage-insensitive CNVs than in dosage-sensitive CNVs. Dosage-sensitive CNVs that are upregulated and downregulated coincide with copy-number increases and decreases. Our results help clarify the relation between CNV dosage and gene expression in the D. melanogaster genome.